Introduction to CBioPortal

Augustin Luna
26 January, 2016

Research Fellow
Department of Biostatistics and Computational Biology
Dana-Farber Cancer Institute

Topics to be Covered

  • CBioPortal overview
  • Data retrieval from CBioPortal using cgdsr
    • List cancer datasets
    • List data types for dataset
    • List case sets
    • Retrieve data for selected genes
    • Retrieve clinical data
  • Plotting retrieved data

What is CBioPortal?

Accessing CBioPortal

CBioPortal Data Types

  • NOTE: Not all samples will have complete data
    • DNA copy number variation
    • mRNA expression
    • microRNA expression
    • Mutation profiles
    • Protein and phosopho-protein expression
    • DNA methylation
    • Limited de-identified clinical data

CBioPortal Data Notes

  • Notes on the available data
  • Example notes
    • Clinical data, includes: overall and disease-free survival, gender, age, stage and tumor grade, when available.
    • mRNA and microRNA data is z-scored (i.e. the number of standard deviations away from the mean of expression

CBioPortal Website Features

CBioPortal Tutorials

CBioPortal Datasets

CBioPortal Home Data Selection

CBioPortal OncoPrint

CBioPortal Plots

CBioPortal Mutations

CBioPortal Survival

CBioPortal OncoPrinter

CBioPortal Mutation Mapper

CBioPortal Study: Summary

CBioPortal Study: Clinical Data

CBioPortal Patient: Summary

CBioPortal Patient: Drug Targets

CBioPortal Patient: Histology

CBioPortal Patient: Pathology

CBioPortal Patient: Copy Number

CBioPortal Patient: Network

What is cgdsr?

Getting Help